Starting phenix.real_space_refine on Fri Feb 14 09:35:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qew_13943/02_2025/7qew_13943.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qew_13943/02_2025/7qew_13943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qew_13943/02_2025/7qew_13943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qew_13943/02_2025/7qew_13943.map" model { file = "/net/cci-nas-00/data/ceres_data/7qew_13943/02_2025/7qew_13943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qew_13943/02_2025/7qew_13943.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 6384 2.51 5 N 1476 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9702 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 6.89, per 1000 atoms: 0.71 Number of scatterers: 9702 At special positions: 0 Unit cell: (96.9, 107.95, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 1758 8.00 N 1476 7.00 C 6384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 72.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'G' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 39 removed outlier: 3.606A pdb=" N PHE G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 44' Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 100 Proline residue: G 87 - end of helix removed outlier: 3.944A pdb=" N ALA G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE G 140 " --> pdb=" O TYR G 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 145 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 158 " --> pdb=" O PHE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 44' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 100 Proline residue: H 87 - end of helix removed outlier: 3.944A pdb=" N ALA H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE H 140 " --> pdb=" O TYR H 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H 141 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 158 " --> pdb=" O PHE H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 15 removed outlier: 4.091A pdb=" N LYS I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 39 through 44' Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 100 Proline residue: I 87 - end of helix removed outlier: 3.944A pdb=" N ALA I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.587A pdb=" N ILE I 140 " --> pdb=" O TYR I 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE I 141 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 158 " --> pdb=" O PHE I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG I 216 " --> pdb=" O TYR I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 44' Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 100 Proline residue: J 87 - end of helix removed outlier: 3.944A pdb=" N ALA J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE J 140 " --> pdb=" O TYR J 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE J 141 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR J 158 " --> pdb=" O PHE J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG J 216 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 15 removed outlier: 4.091A pdb=" N LYS K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 100 Proline residue: K 87 - end of helix removed outlier: 3.944A pdb=" N ALA K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.587A pdb=" N ILE K 140 " --> pdb=" O TYR K 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 141 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 158 " --> pdb=" O PHE K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG K 216 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 39 through 44' Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 100 Proline residue: L 87 - end of helix removed outlier: 3.944A pdb=" N ALA L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE L 141 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR L 158 " --> pdb=" O PHE L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG L 216 " --> pdb=" O TYR L 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 53 600 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2718 1.35 - 1.46: 2633 1.46 - 1.58: 4237 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 9708 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 LMT G 303 " pdb=" C2 LMT G 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C1 LMT J 305 " pdb=" C2 LMT J 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.05e+00 ... (remaining 9703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 12723 1.61 - 3.21: 153 3.21 - 4.82: 63 4.82 - 6.42: 99 6.42 - 8.03: 60 Bond angle restraints: 13098 Sorted by residual: angle pdb=" C6 LMT H 305 " pdb=" C7 LMT H 305 " pdb=" C8 LMT H 305 " ideal model delta sigma weight residual 117.26 109.23 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C6 LMT I 305 " pdb=" C7 LMT I 305 " pdb=" C8 LMT I 305 " ideal model delta sigma weight residual 117.26 109.27 7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C6 LMT J 305 " pdb=" C7 LMT J 305 " pdb=" C8 LMT J 305 " ideal model delta sigma weight residual 117.26 109.28 7.98 3.00e+00 1.11e-01 7.08e+00 angle pdb=" C6 LMT K 305 " pdb=" C7 LMT K 305 " pdb=" C8 LMT K 305 " ideal model delta sigma weight residual 117.26 109.30 7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" C6 LMT L 303 " pdb=" C7 LMT L 303 " pdb=" C8 LMT L 303 " ideal model delta sigma weight residual 117.26 109.31 7.95 3.00e+00 1.11e-01 7.03e+00 ... (remaining 13093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 5056 11.92 - 23.85: 344 23.85 - 35.77: 144 35.77 - 47.70: 42 47.70 - 59.62: 30 Dihedral angle restraints: 5616 sinusoidal: 2298 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ILE J 23 " pdb=" C ILE J 23 " pdb=" N TRP J 24 " pdb=" CA TRP J 24 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 dihedral pdb=" CA ILE I 23 " pdb=" C ILE I 23 " pdb=" N TRP I 24 " pdb=" CA TRP I 24 " ideal model delta harmonic sigma weight residual -180.00 -165.43 -14.57 0 5.00e+00 4.00e-02 8.49e+00 dihedral pdb=" CA ILE H 23 " pdb=" C ILE H 23 " pdb=" N TRP H 24 " pdb=" CA TRP H 24 " ideal model delta harmonic sigma weight residual -180.00 -165.45 -14.55 0 5.00e+00 4.00e-02 8.47e+00 ... (remaining 5613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 764 0.021 - 0.042: 395 0.042 - 0.063: 209 0.063 - 0.084: 51 0.084 - 0.105: 51 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA ILE H 71 " pdb=" N ILE H 71 " pdb=" C ILE H 71 " pdb=" CB ILE H 71 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.76e-01 chirality pdb=" CA PRO J 185 " pdb=" N PRO J 185 " pdb=" C PRO J 185 " pdb=" CB PRO J 185 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.70e-01 chirality pdb=" CA PRO H 185 " pdb=" N PRO H 185 " pdb=" C PRO H 185 " pdb=" CB PRO H 185 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 ... (remaining 1467 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP I 172 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.90e-01 pdb=" N PRO I 173 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO I 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 173 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 172 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO L 173 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO L 173 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 173 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO G 173 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.012 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 455 2.73 - 3.27: 9822 3.27 - 3.82: 15831 3.82 - 4.36: 18958 4.36 - 4.90: 32012 Nonbonded interactions: 77078 Sorted by model distance: nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE L 71 " pdb=" OH TYR L 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE K 71 " pdb=" OH TYR K 158 " model vdw 2.192 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.192 3.040 ... (remaining 77073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 2 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.420 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9708 Z= 0.288 Angle : 0.863 8.031 13098 Z= 0.353 Chirality : 0.035 0.105 1470 Planarity : 0.002 0.025 1542 Dihedral : 11.152 59.620 3414 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 5.36 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1104 helix: 1.43 (0.18), residues: 714 sheet: 4.08 (0.68), residues: 66 loop : -1.08 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 24 HIS 0.001 0.000 HIS H 16 PHE 0.006 0.001 PHE I 51 TYR 0.004 0.001 TYR L 217 ARG 0.001 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 134 TRP cc_start: 0.8079 (m100) cc_final: 0.7759 (m100) REVERT: J 41 LYS cc_start: 0.8219 (tttt) cc_final: 0.7960 (tttp) REVERT: K 41 LYS cc_start: 0.8293 (tttt) cc_final: 0.8012 (tttp) outliers start: 22 outliers final: 1 residues processed: 250 average time/residue: 1.0052 time to fit residues: 273.6172 Evaluate side-chains 193 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.124642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.080734 restraints weight = 14658.772| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.77 r_work: 0.2883 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9708 Z= 0.263 Angle : 0.669 8.606 13098 Z= 0.355 Chirality : 0.044 0.137 1470 Planarity : 0.004 0.024 1542 Dihedral : 9.194 59.856 1400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.27 % Allowed : 12.30 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.25), residues: 1104 helix: 2.35 (0.18), residues: 732 sheet: 3.21 (0.60), residues: 66 loop : -1.04 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 133 HIS 0.007 0.001 HIS G 73 PHE 0.015 0.002 PHE K 31 TYR 0.019 0.002 TYR J 65 ARG 0.009 0.001 ARG I 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6493 (pp-130) REVERT: H 19 SER cc_start: 0.8671 (p) cc_final: 0.8425 (t) REVERT: H 134 TRP cc_start: 0.8146 (m100) cc_final: 0.7781 (m-10) REVERT: I 134 TRP cc_start: 0.8199 (m100) cc_final: 0.7981 (m-10) REVERT: K 41 LYS cc_start: 0.8874 (tttt) cc_final: 0.8619 (tttp) REVERT: K 91 VAL cc_start: 0.8685 (t) cc_final: 0.8485 (m) outliers start: 33 outliers final: 6 residues processed: 217 average time/residue: 1.0463 time to fit residues: 245.8298 Evaluate side-chains 199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078969 restraints weight = 14889.472| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.79 r_work: 0.2849 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9708 Z= 0.319 Angle : 0.677 7.909 13098 Z= 0.355 Chirality : 0.046 0.156 1470 Planarity : 0.003 0.022 1542 Dihedral : 8.882 59.757 1398 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.57 % Allowed : 12.50 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1104 helix: 2.51 (0.18), residues: 738 sheet: 2.77 (0.55), residues: 66 loop : -1.10 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.006 0.001 HIS J 73 PHE 0.016 0.002 PHE L 51 TYR 0.014 0.002 TYR I 65 ARG 0.008 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7755 (tmm-80) REVERT: H 23 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8063 (mp) REVERT: H 134 TRP cc_start: 0.8106 (m100) cc_final: 0.7694 (m-10) REVERT: I 134 TRP cc_start: 0.8136 (m100) cc_final: 0.7877 (m-10) REVERT: K 41 LYS cc_start: 0.8892 (tttt) cc_final: 0.8660 (tttp) REVERT: K 42 GLU cc_start: 0.8397 (pt0) cc_final: 0.8160 (pm20) REVERT: K 209 GLU cc_start: 0.8809 (tp30) cc_final: 0.8578 (tp30) outliers start: 36 outliers final: 19 residues processed: 213 average time/residue: 1.0592 time to fit residues: 244.1395 Evaluate side-chains 202 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.124607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080850 restraints weight = 14590.573| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.76 r_work: 0.2890 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9708 Z= 0.206 Angle : 0.614 8.452 13098 Z= 0.317 Chirality : 0.043 0.142 1470 Planarity : 0.003 0.033 1542 Dihedral : 8.280 59.995 1398 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.77 % Allowed : 13.29 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1104 helix: 2.80 (0.18), residues: 738 sheet: 2.72 (0.54), residues: 66 loop : -1.19 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 133 HIS 0.004 0.001 HIS J 73 PHE 0.020 0.002 PHE J 29 TYR 0.010 0.002 TYR I 65 ARG 0.010 0.001 ARG I 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7806 (tmm-80) REVERT: H 23 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8027 (mp) REVERT: H 134 TRP cc_start: 0.8069 (m100) cc_final: 0.7673 (m-10) REVERT: I 134 TRP cc_start: 0.8114 (m100) cc_final: 0.7849 (m-10) REVERT: I 216 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7340 (tmm-80) REVERT: J 216 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7408 (tmm-80) REVERT: K 216 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7533 (tmm-80) REVERT: L 93 MET cc_start: 0.8106 (mmp) cc_final: 0.7432 (tmm) REVERT: L 216 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7794 (tmm-80) outliers start: 38 outliers final: 24 residues processed: 210 average time/residue: 0.9945 time to fit residues: 226.8706 Evaluate side-chains 209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079523 restraints weight = 14652.130| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.79 r_work: 0.2864 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9708 Z= 0.262 Angle : 0.619 8.026 13098 Z= 0.328 Chirality : 0.044 0.148 1470 Planarity : 0.003 0.021 1542 Dihedral : 8.126 59.747 1398 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.47 % Allowed : 14.38 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.25), residues: 1104 helix: 2.92 (0.18), residues: 738 sheet: 2.63 (0.55), residues: 66 loop : -1.14 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 133 HIS 0.005 0.001 HIS G 73 PHE 0.015 0.002 PHE L 51 TYR 0.015 0.002 TYR H 68 ARG 0.006 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7882 (tmm-80) REVERT: H 22 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7735 (mttp) REVERT: H 23 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8258 (mp) REVERT: H 134 TRP cc_start: 0.8065 (m100) cc_final: 0.7681 (m-10) REVERT: H 216 ARG cc_start: 0.7855 (tmm-80) cc_final: 0.7564 (tmm-80) REVERT: I 134 TRP cc_start: 0.8035 (m100) cc_final: 0.7745 (m-10) REVERT: I 216 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7401 (tmm-80) REVERT: J 216 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7489 (tmm-80) REVERT: K 216 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7635 (tmm-80) REVERT: L 93 MET cc_start: 0.8002 (mmp) cc_final: 0.7365 (tmm) REVERT: L 216 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7895 (tmm-80) outliers start: 35 outliers final: 26 residues processed: 209 average time/residue: 1.1179 time to fit residues: 252.5698 Evaluate side-chains 212 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.124412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080299 restraints weight = 14643.263| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.80 r_work: 0.2884 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9708 Z= 0.215 Angle : 0.620 8.588 13098 Z= 0.321 Chirality : 0.043 0.152 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.867 59.092 1398 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.57 % Allowed : 15.28 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1104 helix: 3.02 (0.18), residues: 738 sheet: 2.62 (0.55), residues: 66 loop : -1.21 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 133 HIS 0.004 0.001 HIS J 73 PHE 0.013 0.001 PHE L 51 TYR 0.012 0.002 TYR K 68 ARG 0.006 0.001 ARG I 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7718 (tmm-80) REVERT: H 22 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7708 (mttp) REVERT: H 23 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8216 (mp) REVERT: H 134 TRP cc_start: 0.8074 (m100) cc_final: 0.7695 (m-10) REVERT: H 216 ARG cc_start: 0.7859 (tmm-80) cc_final: 0.7633 (tmm-80) REVERT: I 134 TRP cc_start: 0.8015 (m100) cc_final: 0.7721 (m-10) REVERT: I 216 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7470 (tmm-80) REVERT: J 216 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7548 (tmm-80) REVERT: K 216 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7667 (tmm-80) REVERT: L 93 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7354 (tmm) REVERT: L 216 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7892 (tmm-80) outliers start: 36 outliers final: 23 residues processed: 207 average time/residue: 1.0742 time to fit residues: 240.2517 Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081116 restraints weight = 14660.000| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.80 r_work: 0.2903 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9708 Z= 0.181 Angle : 0.607 9.584 13098 Z= 0.317 Chirality : 0.041 0.148 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.489 59.548 1398 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.57 % Allowed : 15.28 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.25), residues: 1104 helix: 3.12 (0.18), residues: 738 sheet: 2.66 (0.55), residues: 66 loop : -1.24 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 133 HIS 0.003 0.000 HIS G 73 PHE 0.021 0.001 PHE G 29 TYR 0.010 0.001 TYR H 68 ARG 0.005 0.001 ARG K 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7766 (tmm-80) REVERT: H 23 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8210 (mp) REVERT: H 134 TRP cc_start: 0.8064 (m100) cc_final: 0.7692 (m-10) REVERT: H 216 ARG cc_start: 0.7920 (tmm-80) cc_final: 0.7671 (tmm-80) REVERT: J 216 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7586 (tmm-80) REVERT: K 216 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7681 (tmm-80) REVERT: L 93 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7371 (tmm) outliers start: 36 outliers final: 24 residues processed: 205 average time/residue: 1.0695 time to fit residues: 236.8508 Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081231 restraints weight = 14817.236| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.81 r_work: 0.2905 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9708 Z= 0.178 Angle : 0.626 10.369 13098 Z= 0.322 Chirality : 0.042 0.156 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.230 59.657 1398 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.98 % Allowed : 16.37 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.25), residues: 1104 helix: 3.16 (0.18), residues: 738 sheet: 2.66 (0.56), residues: 66 loop : -1.24 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.003 0.000 HIS J 73 PHE 0.014 0.001 PHE K 29 TYR 0.011 0.001 TYR K 68 ARG 0.005 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7871 (tmm-80) REVERT: H 23 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8233 (mp) REVERT: H 134 TRP cc_start: 0.8051 (m100) cc_final: 0.7666 (m-10) REVERT: H 216 ARG cc_start: 0.7958 (tmm-80) cc_final: 0.7695 (tmm-80) REVERT: J 93 MET cc_start: 0.7766 (ptp) cc_final: 0.7483 (pp-130) REVERT: J 216 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7625 (tmm-80) REVERT: K 216 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7535 (tmm-80) REVERT: L 93 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7312 (tmm) outliers start: 30 outliers final: 21 residues processed: 206 average time/residue: 1.0900 time to fit residues: 242.1042 Evaluate side-chains 208 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 58 optimal weight: 0.0040 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.124718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081187 restraints weight = 14723.169| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.77 r_work: 0.2901 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9708 Z= 0.188 Angle : 0.627 11.088 13098 Z= 0.328 Chirality : 0.042 0.157 1470 Planarity : 0.003 0.019 1542 Dihedral : 7.030 58.837 1398 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.08 % Allowed : 16.27 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.25), residues: 1104 helix: 3.16 (0.18), residues: 738 sheet: 2.64 (0.56), residues: 66 loop : -1.25 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.003 0.001 HIS J 73 PHE 0.030 0.001 PHE J 29 TYR 0.011 0.001 TYR H 68 ARG 0.004 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 154 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8393 (t80) REVERT: G 216 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7898 (tmm-80) REVERT: H 23 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8217 (mp) REVERT: H 134 TRP cc_start: 0.8024 (m100) cc_final: 0.7653 (m-10) REVERT: H 216 ARG cc_start: 0.7955 (tmm-80) cc_final: 0.7685 (tmm-80) REVERT: J 93 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7463 (pp-130) REVERT: J 216 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7520 (tmm-80) REVERT: K 216 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7576 (tmm-80) REVERT: L 93 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7307 (tmm) outliers start: 31 outliers final: 20 residues processed: 210 average time/residue: 1.0789 time to fit residues: 244.9455 Evaluate side-chains 210 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.0370 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081393 restraints weight = 14755.388| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.79 r_work: 0.2906 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9708 Z= 0.178 Angle : 0.644 11.670 13098 Z= 0.329 Chirality : 0.042 0.168 1470 Planarity : 0.003 0.019 1542 Dihedral : 6.811 57.174 1398 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.18 % Allowed : 17.36 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.25), residues: 1104 helix: 3.19 (0.18), residues: 738 sheet: 2.65 (0.56), residues: 66 loop : -1.32 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.003 0.000 HIS J 73 PHE 0.024 0.002 PHE L 29 TYR 0.010 0.001 TYR H 68 ARG 0.004 0.000 ARG J 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 154 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8413 (t80) REVERT: G 216 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7893 (tmm-80) REVERT: H 23 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8239 (mp) REVERT: H 134 TRP cc_start: 0.8010 (m100) cc_final: 0.7637 (m-10) REVERT: H 216 ARG cc_start: 0.7972 (tmm-80) cc_final: 0.7737 (tmm-80) REVERT: J 93 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7481 (pp-130) REVERT: J 216 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7567 (tmm-80) REVERT: K 216 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7583 (tmm-80) REVERT: L 93 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7308 (tmm) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 1.1080 time to fit residues: 243.9600 Evaluate side-chains 204 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081140 restraints weight = 14706.163| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.78 r_work: 0.2905 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9708 Z= 0.185 Angle : 0.634 12.244 13098 Z= 0.331 Chirality : 0.042 0.163 1470 Planarity : 0.003 0.019 1542 Dihedral : 6.625 58.426 1398 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.08 % Allowed : 17.66 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.25), residues: 1104 helix: 3.18 (0.18), residues: 738 sheet: 2.65 (0.56), residues: 66 loop : -1.33 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.003 0.000 HIS J 73 PHE 0.032 0.002 PHE J 29 TYR 0.011 0.001 TYR H 68 ARG 0.004 0.000 ARG J 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10833.19 seconds wall clock time: 191 minutes 16.59 seconds (11476.59 seconds total)